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10 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
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PYM1
PYM1 exon junction complex associated factor
Chromosome 12 · 12q13.2
NCBI Gene: 84305Ensembl: ENSG00000170473.18HGNC: HGNC:30258UniProt: Q9BRP8
88PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
exon-exon junction complexprotein bindingribosome bindingnuclear-transcribed mRNA catabolic process, nonsense-mediated decayAlzheimer diseasecardiac arrestcancerneoplasm
✦AI Summary

PYM1 is a critical regulator of the exon junction complex (EJC), a multiprotein assembly deposited upstream of exon-exon junctions during pre-mRNA splicing 1. PYM1 functions as an EJC disassembly factor that operates through two distinct mechanisms: it mediates translation-independent EJC destabilization by binding to the EJC core proteins MAGOH-Y14, while the elongating ribosome itself handles translation-dependent removal 2. Additionally, PYM1 bridges the EJC and translation machinery by simultaneously binding the Y14-magoh complex and the 40S ribosomal subunit, enhancing translation of spliced mRNAs 3. PYM1 acts as an EJC specificity factor by limiting non-canonical EJC occupancy, particularly on transcripts with few or long exons, thereby tuning mRNA expression patterns 4. Functionally, PYM1 antagonizes nonsense-mediated decay (NMD) and facilitates EJC protein recycling 1. Disease relevance emerges from flavivirus infection: dengue, West Nile, and Zika viruses exploit PYM1 through capsid-protein interactions to disrupt EJC function and NMD, protecting viral RNA from degradation and enhancing infection 5. This viral hijacking of PYM1 reshapes host mRNA regulation, making PYM1 an antiviral target conserved across multiple flaviviruses.

Sources cited
1
PYM1 limits non-canonical EJC occupancy to tune mRNA expression and acts as an EJC specificity factor hijacked by flaviviruses
PMID: 40885765
2
PYM1 mediates translation-independent EJC destabilization and prevents non-canonical EJC binding
PMID: 40161626
3
Flavivirus capsids interact with PYM1 to inhibit NMD and EJC function, protecting viral RNA from decay
PMID: 30833725
4
PYM acts as an EJC disassembly factor by binding MAGOH-Y14, antagonizes NMD, and impairs EJC recycling when depleted
PMID: 19410547
5
PYM bridges the EJC and translation machinery by binding Y14-magoh and the 40S ribosomal subunit to enhance translation of spliced mRNAs
PMID: 18026120
Disease Associationsⓘ20
Alzheimer diseaseOpen Targets
0.05Suggestive
cardiac arrestOpen Targets
0.03Suggestive
cancerOpen Targets
0.02Suggestive
neoplasmOpen Targets
0.02Suggestive
esophageal cancerOpen Targets
0.02Suggestive
hepatocellular carcinomaOpen Targets
0.02Suggestive
tongue cancerOpen Targets
0.02Suggestive
rheumatoid arthritisOpen Targets
0.01Suggestive
hemangiomaOpen Targets
0.01Suggestive
breast cancerOpen Targets
0.01Suggestive
oral squamous cell carcinomaOpen Targets
0.01Suggestive
viral diseaseOpen Targets
0.01Suggestive
ulcerative colitisOpen Targets
0.01Suggestive
infectionOpen Targets
0.01Suggestive
lip and oral cavity carcinomaOpen Targets
0.01Suggestive
prostate cancerOpen Targets
0.01Suggestive
Venous malformationOpen Targets
0.01Suggestive
melanomaOpen Targets
0.01Suggestive
colon carcinomaOpen Targets
0.00Suggestive
osteoporosisOpen Targets
0.00Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
MAGOHBProtein interaction95%MAGOHProtein interaction90%UPF1Protein interaction90%RBM8AProtein interaction90%CASC3Protein interaction90%UPF2Protein interaction90%
Tissue Expression6 tissues
Liver
100%
Lung
60%
Heart
43%
Bone Marrow
41%
Ovary
41%
Brain
36%
Gene Interaction Network
Click a node to explore
PYM1MAGOHBMAGOHUPF1RBM8ACASC3UPF2
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted · UniProt Q9BRP8
View on AlphaFold ↗
Constraintⓘ
LOEUFⓘ
0.62LoF Tolerant
pLIⓘ
0.79Intermediate
Observed/Expected LoF0.33 [0.19–0.62]
RankingsWhere PYM1 stands among ~20K protein-coding genes
  • #5,440of 20,598
    Most Researched88
  • #4,343of 17,882
    Most Constrained (LOEUF)0.62 · top quartile
Genes detectedPYM1
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
PYM1 limits non-canonical Exon Junction Complex occupancy in a gene architecture dependent manner to tune mRNA expression.
PMID: 40885765
Nat Commun · 2025
1.00
2
Identification of antiviral roles for the exon-junction complex and nonsense-mediated decay in flaviviral infection.
PMID: 30833725
Nat Microbiol · 2019
0.90
3
PYM1 limits non-canonical Exon Junction Complex occupancy in a gene architecture dependent manner to tune mRNA expression.
PMID: 40161626
bioRxiv · 2025
0.80
4
ORF57: Master regulator of KSHV mRNA biogenesis.
PMID: 20686356
Cell Cycle · 2010
0.70
5
Disassembly of exon junction complexes by PYM.
PMID: 19410547
Cell · 2009
0.60